Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 5Y1Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLY* 3.7 11.7 - - - -
4A VAL* 3.5 39.9 + - + -
34A TYR* 2.8 32.6 + + - +
39A ASP* 4.0 22.3 + - - -
65A TYR* 3.9 2.5 - - - +
94A ARG* 4.7 1.8 - - - -
97A ALA* 3.5 22.6 + - + +
98A CYS* 2.8 20.5 + - - +
100A SER* 1.3 86.2 + - - +
102A VAL* 1.3 64.2 + - - +
103A ALA 3.2 2.5 - - - -
104A LYS* 2.9 18.7 + - + +
105A VAL* 2.9 13.3 + - + +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 4.0 9.6 - - + +
82A LEU* 4.5 6.4 - - + +
84A ASN* 3.4 37.5 - - + +
98A CYS 3.9 8.5 - - - +
99A ALA* 3.4 21.3 + - - +
101A HIS* 1.3 76.7 - - - +
103A ALA* 1.3 64.3 + - - +
105A VAL* 3.0 10.0 + - - +
106A ALA* 2.9 20.8 + - - +
115A ILE* 3.8 35.9 - - + -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 4.9 1.0 + - - -
100A SER 4.9 4.0 + - - +
101A HIS 3.2 0.8 - - - -
102A VAL* 1.3 79.5 - - - +
104A LYS* 1.3 57.9 + - - +
106A ALA* 3.3 7.5 + - - +
107A GLU* 2.9 29.4 + - - +
115A ILE* 5.6 2.5 - - - -
164C LYS* 5.8 5.6 - - - +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA 3.0 26.3 + - - -
3A GLY* 4.3 1.0 - - - -
4A VAL* 3.3 37.7 + - + +
6A PHE* 3.7 13.2 - - + -
100A SER 5.1 4.0 + - - +
101A HIS* 2.9 14.7 + - + +
103A ALA* 1.3 79.8 - - - +
105A VAL* 1.3 55.4 + - - +
107A GLU* 3.3 8.7 + - + +
108A PHE* 2.9 27.4 + - - +
247C HIS* 4.2 14.1 + - + +
251C GLU* 5.9 0.6 + - - -
312C ASP* 5.1 13.5 - - + +
313C ARG 6.1 0.4 - - - +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.2 8.1 - - + -
6A PHE* 3.9 20.2 - - + -
41A LEU* 4.1 9.6 - - + -
65A TYR* 4.0 44.4 - - + -
82A LEU* 4.1 13.2 - - + -
101A HIS* 2.9 15.5 + - + +
102A VAL* 3.0 9.2 + - - +
104A LYS* 1.3 72.9 - - - +
106A ALA* 1.3 65.8 + - - +
108A PHE* 3.0 10.1 + - - +
109A PHE* 3.0 38.3 + - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 4.1 7.4 - - + +
102A VAL 2.9 12.6 + - - +
103A ALA* 3.7 9.2 - - - +
105A VAL* 1.3 77.8 - - - +
107A GLU* 1.3 62.6 + - - +
108A PHE 3.5 0.2 + - - -
109A PHE* 3.5 17.9 - - - +
110A GLN* 4.0 3.6 + - - -
111A GLY 4.8 0.5 + - - -
112A VAL* 4.1 23.8 + - + +
115A ILE* 4.0 23.6 - - + -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ALA 2.9 16.5 + - - +
104A LYS* 3.6 9.9 - - + +
105A VAL 3.1 0.2 - - - -
106A ALA* 1.3 78.8 - - - +
108A PHE* 1.3 62.8 + - - +
110A GLN* 2.7 37.2 + - - +
269C TRP* 3.7 23.0 + - + -
310C GLN 3.4 8.0 - - - +
311C HIS* 2.8 44.1 + - + -
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.4 55.6 - + + -
10A ARG* 3.7 20.4 - - + -
13A LEU* 4.2 9.2 - - + -
14A LEU* 3.5 40.3 - - + +
17A TYR* 5.2 0.7 - - - -
104A LYS 2.9 13.2 + - - +
105A VAL 3.0 8.0 + - - +
107A GLU* 1.3 79.1 - - - +
109A PHE* 1.3 86.7 + + - +
110A GLN* 3.2 6.8 + - - +
310C GLN* 3.6 50.0 + - + +
312C ASP* 4.0 4.0 - - + -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 11.2 - - + -
14A LEU* 4.6 0.2 - - + -
17A TYR* 3.6 36.6 - + + -
32A TYR* 3.3 58.3 - + - -
41A LEU* 4.4 10.5 - - + -
65A TYR* 5.7 0.2 - - + -
67A PHE* 3.8 16.4 - + + -
82A LEU* 5.2 4.0 - - + -
105A VAL* 3.0 41.6 + - + +
106A ALA 3.5 7.5 - - - +
108A PHE* 1.3 105.2 - + + +
110A GLN* 1.3 69.2 + - - +
111A GLY 3.4 1.2 + - - -
112A VAL* 3.6 14.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il